BioC 2.10: CHECK report for Rgraphviz on lamb2

Package: Rgraphviz

Version: 1.34.2

Command: /home/biocbuild/bbs-2.10-bioc/R/bin/R CMD check --no-vignettes --timings Rgraphviz_1.34.2.tar.gz

StartedAt: 2012-09-24 03:19:59 -0700 (Mon, 24 Sep 2012)

EndedAt: 2012-09-24 03:20:49 -0700 (Mon, 24 Sep 2012)

EllapsedTime: 50.3 seconds

RetCode: 0

Status: OK

CheckDir: Rgraphviz.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.10-bioc/meat/Rgraphviz.Rcheck’
* using R version 2.15.1 (2012-06-22)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rgraphviz/DESCRIPTION’ ... OK
* this is package ‘Rgraphviz’ version ‘1.34.2’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking whether package ‘Rgraphviz’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

* installing *source* package ‘Rgraphviz’ ...
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for stdbool.h that conforms to C99... yes
checking for _Bool... yes
checking for whether compiler has bool... yes
configure: No --with-graphviz option was specified. Trying to find Graphviz using other methods.
checking for pkg-config... /usr/bin/pkg-config
configure: Found Graphviz version '2.26.3'.
configure: Graphviz major version is '2' and minor version is '26'.
configure: Using the following compilation and linking flags for Rgraphviz
configure:    PKG_CPPFLAGS=-I/usr/include/graphviz  
configure:    PKG_LIBS=-lgvc -lgraph -lcdt  
configure:    GVIZ_DEFS= -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=26 
configure: Setting Graphviz Build version to '2.26.3'.
configure: creating ./config.status
config.status: creating R/graphviz_build_version.R
config.status: creating src/Makevars
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/include/graphviz    -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=26  -I/usr/local/include    -fpic  -g -O2  -Wall -c LL_funcs.c -o LL_funcs.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/include/graphviz    -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=26  -I/usr/local/include    -fpic  -g -O2  -Wall -c Rgraphviz.c -o Rgraphviz.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/include/graphviz    -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=26  -I/usr/local/include    -fpic  -g -O2  -Wall -c RgraphvizInit.c -o RgraphvizInit.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/include/graphviz    -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=26  -I/usr/local/include    -fpic  -g -O2  -Wall -c agopen.c -o agopen.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/include/graphviz    -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=26  -I/usr/local/include    -fpic  -g -O2  -Wall -c agread.c -o agread.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/include/graphviz    -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=26  -I/usr/local/include    -fpic  -g -O2  -Wall -c agwrite.c -o agwrite.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/include/graphviz    -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=26  -I/usr/local/include    -fpic  -g -O2  -Wall -c bezier.c -o bezier.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/include/graphviz    -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=26  -I/usr/local/include    -fpic  -g -O2  -Wall -c buildEdgeList.c -o buildEdgeList.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/include/graphviz    -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=26  -I/usr/local/include    -fpic  -g -O2  -Wall -c buildNodeList.c -o buildNodeList.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/include/graphviz    -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=26  -I/usr/local/include    -fpic  -g -O2  -Wall -c doLayout.c -o doLayout.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/include/graphviz    -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=26  -I/usr/local/include    -fpic  -g -O2  -Wall -c graphvizVersion.c -o graphvizVersion.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG -I/usr/include/graphviz    -DHAVE_STDBOOL_H=1 -DHAVE_BOOL=1 -DGRAPHVIZ_MAJOR=2 -DGRAPHVIZ_MINOR=26  -I/usr/local/include    -fpic  -g -O2  -Wall -c init.c -o init.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o Rgraphviz.so LL_funcs.o Rgraphviz.o RgraphvizInit.o agopen.o agread.o agwrite.o bezier.o buildEdgeList.o buildNodeList.o doLayout.o graphvizVersion.o init.o -lgvc -lgraph -lcdt -L/home/biocbuild/bbs-2.10-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.10-bioc/meat/Rgraphviz.Rcheck/Rgraphviz/libs
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘head’ from package ‘utils’ in package ‘Rgraphviz’
Creating a generic function for ‘tail’ from package ‘utils’ in package ‘Rgraphviz’
Creating a generic function for ‘lines’ from package ‘graphics’ in package ‘Rgraphviz’
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘Rgraphviz.Rnw’ 
   ‘newRgraphvizInterface.Rnw’ 
** testing if installed package can be loaded

* DONE (Rgraphviz)

name	user	system	elapsed
AgEdge-class	0.040	0.012	0.049
AgNode-class	0.012	0.000	0.013
AgTextLabel-class	0.032	0.000	0.031
BezierCurve-class	0.008	0.004	0.016
GraphvizLayouts	0.008	0.000	0.008
Ragraph-class	0.052	0.000	0.057
agopen	0.024	0.000	0.036
agopenSimple	0.140	0.004	0.142
agwrite	0.012	0.000	0.011
boundingBox-class	0.008	0.000	0.009
buildNodeList	0.008	0.000	0.007
clusterData-methods	0.368	0.016	0.492
getDefaultAttrs	0.000	0.000	0.001
graphLayout	0.012	0.000	0.012
graphvizVersion	0.000	0.000	0.001
layoutGraph	0.196	0.000	0.193
makeNodeAttrs	0.004	0.000	0.005
pEdge-class	0.008	0.000	0.008
pNode-class	0.004	0.000	0.006
pieGlyph	0.012	0.000	0.013
plot-methods	0	0	0
removedEdges	0.008	0.000	0.007
renderGraph	0.288	0.008	0.300
toDot-methods	0.016	0.004	0.016
toFile	0.092	0.000	0.101
xyPoint-class	0.004	0.000	0.002

Summary

Command output